A syntenic map of over 100 genetic loci has been achieved for the domestic cat containing Type I (coding gene) markers on 17 of the 19 cat chromosomes. The map was built using somatic cell hybrid panels, high resolution G-banding karyology, fluorescence in situ hybridization, and pedigree analysis. Alignment of linkage position of feline with human loci revealed extensive syntenic conservation of the feline and human genomes, in several cases spanning entire chromosomes. In- depth analysis of linkage and genomic organization (including molecular cloning, gene mapping, sequence analysis) was undertaken for the following gene families: (1) FLA, feline major histocompatibility complex; (2) feline homeobox genes; (3) sex determination genes, SRY, ZFY and ZFX; (4) endogenous retroviral family, RD114 and FeLV; (5) proto-oncogenes and viral integration sites; and (6) coat color genes. In collaboration with leading comparative gene mappers in mouse and cattle, we have identified 321 Type I (coding gene) marker anchor loci for use in comparative mapping for all species. Anchor loci were selected to provide a 5-10 centiMorgans density of gene markers for use in comparing genomic segments for all mammalian species' gene maps. In order to construct a genetic linkage map of the cat, we initiated inter-species sexual crosses and back-crosses between domestic cat and Asian leopard cat (Prionailurus bengalensis). This species was selected because of a substantive evolutionary genetic distance plus our ability to make fertile F1 females. Over 80 F1 individuals were produced, primarily by artificial insemination, and over 48 back-cross individuals have been born. The interspecies back-cross was used to construct a comparative anchor locus map of feline chromosome B4 which is homologous to human chromosome 12. M13 libraries of cat DNA have been used to screen for hypervariable short tandem repeat polymorphism (STRP) also called microsatellite loci. To date 300 have been sequenced, polymerase chain reaction primers designed, and STRP markers are now being mapped on the interspecies back-cross.